rs4054823

Variant names:

• chr17-13721707-T-C
• rs4054823

Your query was ambiguous. Multiple possible variants found:

• chr17-13721707-T-C
• chr17-13721707-T-G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.426 in 151,954 control chromosomes in the GnomAD database, including 14,141 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.43 (14141 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 36 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64739 AN: 151836 Hom.: 14130 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.420

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.426 AC: 64789 AN: 151954 Hom.: 14141 Cov.: 32 AF XY: 0.431 AC XY: 31998 AN XY: 74264

African (AFR) AF: 0.319 AC: 13207 AN: 41440

American (AMR) AF: 0.476 AC: 7269 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1607 AN: 3470

East Asian (EAS) AF: 0.524 AC: 2694 AN: 5144

South Asian (SAS) AF: 0.474 AC: 2283 AN: 4814

European-Finnish (FIN) AF: 0.493 AC: 5203 AN: 10550

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31085 AN: 67958

Other (OTH) AF: 0.421 AC: 887 AN: 2108

Alfa AF: 0.446 Hom.: 29909

Bravo AF: 0.419

Asia WGS AF: 0.485 AC: 1688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	22
DANN	Benign	0.83
PhyloP100		1.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4054823; hg19: chr17-13625024;